11-5145895-C-T

Variant names:

• chr11-5145895-C-T
• rs2472523

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.307 in 151,526 control chromosomes in the GnomAD database, including 8,375 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.31 (8375 hom., cov: 31)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.142
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.428 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.307 AC: 46533 AN: 151412 Hom.: 8380 Cov.: 31

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.708

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.442

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.439

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.386

Gnomad OTH AF: 0.304

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.307 AC: 46521 AN: 151526 Hom.: 8375 Cov.: 31 AF XY: 0.310 AC XY: 22950 AN XY: 74050

African (AFR) AF: 0.111 AC: 4574 AN: 41368

American (AMR) AF: 0.322 AC: 4899 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.342 AC: 1182 AN: 3460

East Asian (EAS) AF: 0.443 AC: 2286 AN: 5162

South Asian (SAS) AF: 0.298 AC: 1430 AN: 4806

European-Finnish (FIN) AF: 0.439 AC: 4545 AN: 10350

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.386 AC: 26211 AN: 67846

Other (OTH) AF: 0.302 AC: 636 AN: 2108

Alfa AF: 0.360 Hom.: 17678

Bravo AF: 0.292

Asia WGS AF: 0.328 AC: 1129 AN: 3444

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.1
DANN	Benign	0.51
PhyloP100		-0.14

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2472523; hg19: chr11-5167125;